An interview with Dr Jean-Marc Daran
Dr Jean-Marc Daran is Associate Professor and Section Leader at the Department of Biotechnology of the Delft University of Technology. In this interview, he tells us more about his research on systems, genomic and synthetic biology, and why he thinks microbiology matters.
Tell us about your research.
I’m an Associate Professor and for about a year, I have led the industrial microbiology section at the biotechnology department, a group that I am running with three other academic staff members. The overarching theme of research carried out within industrial microbiology seeks to understand how micro-organisms perform in existing and novel industrial processes and based on this understanding; seeks to improve microbial performance and design new microbial processes.
Our research is based on the integration of quantitative physiology (systems biology) with molecular techniques (genomics, synthetic biology). Our model organisms are mostly yeasts, including laboratory and industrial strains of Saccharomyces cerevisiae, hybrid brewing strains of Saccharomyces pastorianus and ‘non-conventional’ yeast species (e.g., Ogataea polymorpha, Kluyveromyces marxianus, Yarrowia lipolytica). In addition, we regularly work on other microbes, ranging from the antibiotic-producing fungus Penicillium chrysogenum to acetic acid bacteria.
What is your area of specialism and why is it important?
Our industrialised society faces the essential challenge to replace oil-based industries and derived products by providing sustainable alternatives. This poses new scientific challenges to industrial microbiology research. Micro-organisms are already indispensable for the large-scale production of fermented food products, chemicals and biofuels. The construction of efficient cell factories, ability to produce new molecules at near-theoretical yields from low-grade, non-food feedstocks, requires us to decipher the complex genome of industrial strains and to reprogram complicated metabolic and regulatory networks. The design and construction of such robust and versatile, ‘next generation’ cell factories involves a profound and fundamental understanding of the native networks in an industrial micro-organism. In this context my research interest can be explained as follows:
Increase the molecular toolbox for genetic analysis and modification of micro-organisms.
- Implement CRISPR-Cas9 in eukaryotic industrial organisms.
- Design, engineer and control complex genetic networks.
Improving microbial performance by applying engineering principles (design, build, test).
- Improving cell robustness in industrial fermentations by alleviating B-vitamin requirement and expanding enzymatic repertoire by engineering new co-factors in Saccharomyces cerevisiae.
- Flavour formation in Saccharomyces and Kluyveromyces species.
- Production of high added-value plant-derived secondary metabolites in S. cerevisiae.
Understand the link between the genome complexity and industrial performance of lager brewing yeasts.
- Decipher the genome complexity of S. pastorianus hybrids.
- Analyse and understand phenotypic and genotypic variations in S. pastorianus populations.
- Improve industrial strain performance and implementation of new strains.
What are the most important skills you need for your current role?
First and foremost, you need to be curious; curiosity is the key for innovation and keeping your curiosity level high is demanding. Nowadays, academic work is not only limited to education and research; you must have a broad range of skills. You have to be an accountant, a psychologist, a manager, a jurist, etc…and have the ability to switch cap quickly.
What qualifications did you obtain before starting this role?
Before joining the Delft University of Technology, I obtained an engineering degree and a PhD in Microbiology from the National Institute of Applied Sciences in Toulouse, France. After a short stay in Manchester as a postdoc, I moved to industry for seven years. Eventually, I started my academic career in 2003 in Delft.
What professional challenges do you face and how do you try to overcome them?
Yeast biotechnology is a competitive field, and you have to be reactive and stay innovative to avoid being scooped by others. Coping quickly with new technological development is critical to remaining on the front-line. The arrival of CRISPR-Cas, a molecular Swiss army knife, allowed us to construct yeast strains that we would not have even dreamed of five years ago, because the genetics would have been too much hassle.
To be able to achieve this, you have to be able to create a co-operative team atmosphere and encourage synergy between group members. Leading a large group of smart people is not always an easy task.
What is a typical working day for you?
A typical day at work includes meetings with PhDs, other PIs, supporting staff, answering and sending emails, as well as preparing and giving lectures. But often you have to improvise, as a solution to something unexpected has to be found. Writing, editing manuscripts, reports or proposals, is unfortunately regularly an outside working hours activity.
Tell us about your biggest professional achievement(s) so far.
I am really proud of my achievements and I find it difficult to single out one item. But Delft is a University of Technology and many of our graduates and PhDs continue their careers in industry. It’s a great reward to have, when years later you get the opportunity to collaborate with them again. Witnessing their successful professional career is likely my greatest personal achievement.
Please tell us a little about the educational and outreach activities you undertake in your role.
I teach molecular biology and genomics in the department of Life Science and Technology at the Delft University of Technology. I am always pleased when I meet a former student at a company, university, or elsewhere. Our MSc programme is very much influenced by our most recent research and inspires many MSc students to follow a research path and embark on applying for a PhD programme.
Communicating your results to a wider audience is an important function of scientists. Recent works on CRISPR mechanisms, evolution and the origin of lager brewing yeasts have received some media attention, as they have been the subject of articles in national newspapers. I like the idea that everyone can read an article introducing a complex notion, such as gene neofunctionalization while having breakfast.
Where did your interest in microbiology come from?
I do not really remember; I have the impression that I've been familiar with yeast since I was a little boy. My father was a baker and I vividly remember this strong, addictive smell of fresh yeast. So maybe, I was made to be a microbiologist. At University my favourite class was applied microbiology, which presented how you could use microbes to produce molecules such food, drugs, fuels.
Why does microbiology matter?
Yeasts and industrial micro-organisms are essential to keep up our way of life. Without them there would be no bread, yogurt, cheese, wine, or beer. We may not have domesticated these microbes; they may have domesticated us. But the role of microbes will become more and more important, in a society that has to transition from oil-based industries and derived products, to sustainable alternatives. So far, a minute number of species are used, and successful transition will require a much deeper exploration of the microbial world.
